The detection of specific nucleic acids is an important tool for diagnostic medicine and molecular biology research. Gene probe assays currently play roles in identifying infectious organisms such as bacteria and viruses, in probing the expression of normal genes and identifying mutant genes such as oncogenes, in typing tissue for compatibility preceding tissue transplantation, in matching tissue or blood samples for forensic medicine, and for exploring homology among genes from different species.
Ideally, a gene probe assay should be sensitive, specific and easily automatable (for a review, see Nickerson, Current Opinion in Biotechnology 4:48-51 (1993)). The requirement for sensitivity (i.e. low detection limits) has been greatly alleviated by the development of the polymerase chain reaction (PCR) and other amplification technologies which allow researchers to amplify exponentially a specific nucleic acid sequence before analysis (for a review, see Abramson et al., Current Opinion in Biotechnology, 4:41-47 (1993)).
There is a variety of detection methods that have been developed to detect the product resulting from PCR amplification. Detection can be achieved directly by incorporating signal generating nucleotide analogues during the PCR reaction, or indirectly, e.g., such as by hybridization with nucleic acid probes having incorporated signal generating nucleotide analogues. In either approach, there is a need for having sensitive and stable nucleotide analogues, which ideally could be detected automatically. To that end, fluorescent tagging, with its advantages of high sensitivity and multicolor detection, had been developed and quickly came to dominate applications in nucleic acid sequencing and microarray expression analysis. A broad variety of fluorescent-tagged NTPs, dNTPs and ddNTPs are commercially available.
An alternative to fluorescence based detection is electrochemical detection (“ECD”), which can be highly sensitive, rapid and amenable to inexpensive production in miniaturized (“lab-on-a-chip”) formats. Most electrochemical applications are based upon introducing one or more copies of a conjugated redox label, typically metal complexes, metallocenes or quinines. As with different fluor compounds, redox labels are also available that have different redox potentials, which makes them attractive candidates for multiplex nucleic acid detection and sequencing should they be sufficiently integrateable or conjugatable into a growing nucleic acid chain, synthetically or naturally.
One approach has been to use ferrocene or its derivatives as label agents. In this approach, ferrocene-containing labeling agents and oligonucleotides are synthesized separately. Then the ferrocene-containing labeling agent is used to end-label the oligos at either the 5′ or 3′ end. For example, see Brown et al., Metalloorganic labels for DNA sequencing and mapping, New Journal of Chemistry, 18:317-326 (1994).
In early demonstrations of ferrocene tagging, 5′-aminohexyl oligonucleotides were chemically conjugated with carboxyl derivatives of ferrocene to enable electrochemical detection (“ECD”) of hybridization and PCR amplicons at femtomole levels. See Takenaka et al., Electrochemically active DNA probes: detection of target DNA sequences at fermtomole level by high-performance liquid chromatography with electrochemical detection, Analytical Biochemistry, 218: 436-443 (1994); Ihara et al., Ferrocene-oligonucleotide conjugates for electrochemical probing of DNA. Nucleic Acids Research 24: 4273-4278 (1996); and Uto et al., Electrochemical analysis of DNA amplified by the polymerase chain reaction with a ferrocenylated oligonucleotide, Analytical Biochemistry, 250: 122-124 (1997).
Such ferrocene labeling can also be used for internal labeling. Internal post-synthetic labeling of DNA probes has been obtained by reaction with ferrocene carboxaldehyde or aminoferrocene. See Xu et al., Electrochemical detection of sequence-specific DNA using a DNA probe labeled with aminoferrocene and chitosan modified electrode immobilized with ssDNA. Analyst, 126:62-65 (2001).
Alternatively, ferrocene labeling agent can be used for incorporation during chemical oligonucleotide synthesis. Ferrocene phosphoramidites and monomers with a ferrocenyl moiety linked to position 5 of 2′-dU or the 2′-sugar position of dA and dC have been described, as has on-column derivatization of iodo-dU with ferrocenyl propargylamide. See Wlassoff and King, Ferrocene conjugates of dUTP for enzymatic redox labelling of DNA, Nucleic Acids Research, 30:e58 (2002) and references therein, all expressly incorporated by reference.
For example, Navarro et al. developed bisfunctional ferrocene containing phosphoramidite and dimethoxytrityl (“DMT”) group, and used them in an automated solid-phase DNA synthesizer using phosphoramidite chemistry. Navarro et al., Automated synthesis of new ferrocenyl-modified oligonucleotides: study of their properties in solution, Nucleic Acids Research, 32:5310-5319 (2004). However, such compounds have lower coupling yield. The A, T, C and G synthons classically reacted with an average coupling yield of 98% (measured via DMT quantification). In comparison, the coupling yield for the bifunctional ferrocene compound 2, as shown below, was 95% from DMT quantification, and the coupling yield of compound 1, also shown below, was even lower, estimated to be 80%. Such low coupling yield renders them inadequate for routine DNA synthesis.

In routine automatic nucleic acids synthesis, high average stepwise yield is crucial. Coupling efficiency has dramatic effect on the overall yield, as illustrated in Table 1.
TABLE 1The relationship between coupling efficiencyand yield in DNA synthesisOligonucleotideCoupling efficiencylength90%95%97%98.5%99.5%10mer38.763.076.087.395.620mer13.537.756.175.090.950mer—8.1022.547.778.2100mer——4.9022.460.88
As can be seen, the effect of coupling efficiency on the overall yield is much greater for longer sequence, and an average stepwise yield less than 98% is totally unacceptable for routine oligonucleotide synthesis. See Brown and Brown, Modern machine-aided methods of oligoxyribonucleotide synthesis, in Oligonucleotides and Analogues: A Practical Approach, Ed. Eckstein, IRL Press, Oxford UK (1991), herein expressly incorporated by reference. As such the available ferrocene derivatives, such as those reported by Navarro et al. are not useful in routine DNA synthesis.
There have also been attempts to develop ferrocene-containing nucleotide analogues for incorporation of ferrocene labels into DNA by polymerases. For such purpose, ferrocene-containing dUTPs were developed by tagging ferrocene to the 5 position of the base of dUTP. Such analogue could be incorporated as dTTP substitutes using different polymerases. However, such analogues only have rather low incorporation efficiency and lead to pre-mature termination. For example, in a PCR reaction, the analogues have to be doped with normal dTTP for chain growth. There was no amplicon obtained when only analogues were used. See Wlassoff and King, Ferrocene conjugates of dUTP for enzymatic redox labelling of DNA, Nucleic Acids Research, 30:e58 (2002) and references therein, all expressly incorporated by reference. It is unclear whether such analogues could result in coupling efficiency high enough for routine automated DNA synthesis. However, given the low incorporation efficiency demonstrated in polymerase synthesis, it is doubtful such analogues will have coupling efficiencies high enough for routine DNA synthesis. New analogues with higher coupling efficiency are therefore needed.
We previously described two such analogues, N6 and W97, which are ferrocene nucleosides. See US publications 20030232354 and 20030143556, each entitled “Nucleic acid reactions using labels with different redox potentials.” However, the “bases” in those labels contribute to nonspecific binding background and regioisomers that are difficult to synthesize and purify, and that are unnecessary in end-labeling applications, where hybridization functionality is not necessarily needed. Moreover, when ferrocene is used as the label, hydrophobicity can be a problem.
It is an object of the invention to develop “baseless” labels conducive to lessening one or more of the above drawbacks.